From owner-acedb@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!sprout.nal.usda.gov!usenet From: Doug Bigwood Newsgroups: bionet.software.acedb Subject: ACE97 Program and Schedule Date: Fri, 02 May 1997 11:16:30 -0400 Organization: Genome Informatics Group, University of Maryland Lines: 136 Message-ID: <336A054E.1382@gig.usda.gov> NNTP-Posting-Host: locus.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) The ACE97 Program and Schedule (tentative) is now available at http://probe.nalusda.gov:8000/ace97/ace97program.html. A copy is also appended to this message. Note that the organizers are looking for tutorial speakers for the following subjects: ACEDB Query Language, Tablemaker, Map Displays, and the Sequence Display. If you are willing to give a tutorial on one of these subjects, or are willing to present a tutorial on a subject not listed in the program, please contact Doug Bigwood at dbigwood@gig.usda.gov. Also, some likely participants have been asking about registration for the conference. Dave Matthews is working feverishly to pin down the exact costs and requirements and he hopes to have this information very soon. The organizers want to keep the costs low and thanks to funding from USDA,NAL and Cornell we will be able to do this. We will post a message to this newsgroup when registration opens. We do know that registraton will close on July 7, so there will be plenty of time. ==================================================================== ACE97 Program and Schedule Summary: July 7: Last day to Register July 26: Arrival July 27: Tutorials July 28, 29: Conference July 30 - August 8: Workshop August 9: Meeting review and planning of ACE98 Saturday, July 26 Arrival. Sunday, July 27 Tutorials (tentative) - there will be four slots, 2 morning and 2 afternoon - the tutorials will be scheduled according to interest to minimize conflicts. New Curators - How to Create an ACeDB Database. Sam Cartinhour Advanced Curators - How to make use of ACeDB displays. (Unknown) Part 1 - Map displays Part 2 - Sequence display An Introduction to Java and Applets. John Morris ACeDB for Windows. Richard Bruskiewich Setting up a WWW interface to ACEDB Part 1 - Setting up an aceserver. Curt Jamison Part 2 - Webace, A Web Interface for ACeDB databases - Steve Beckstrom-Sternberg Acembly, Sequence Assembly Program - Jean Thierry-Mieg GeneFinder and ACeDB - Richard Durbin Querying the ACEDB query language tablemaker All day: Poster Setup Monday, July 28 Opening remarks - Dave Matthews and Doug Bigwood Morning Program What's New with ACeDB - Richard Durbin and Jean Thierry-Mieg and others ... Afternoon Program more ... All day: Poster viewing Evening: Welcome Barbeque (transportation provided) Tuesday, July 29 Morning Program Afternoon Program Panel Discussion: ACEDB - Where do we go from here? Moderator: Doug Bigwood All day: Poster viewing Wednesday, July 30 Morning Working Groups Convene Possible working groups (anyone will be able to form a working group) Curators (build and enhance your databases) Query Language Comparative Map Displays Java and ACEDB Displays Java Beans and components New/Modified Displays Client/Server communications Java 1.1 features More ... ??? Object Brokering/Exchange Documentation Windows ACEDB MacACE Data verification and validation tools Afternoon Working groups report on direction the group will take for the rest of the workshop Thursday, July 31 - Friday, August 8 Morning Working Groups report on progress Tuesday, August 5 18:00 - 21:00 - Banquet, Clark Hall Friday, August 8 Afternoon Working Groups present and submit final reports Saturday, August 9 Morning Meeting review and planning of next meeting From owner-acedb@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!biochem.umass.edu!bscott From: bscott@biochem.umass.edu (Brian Scott) Newsgroups: bionet.software.acedb Subject: Free Workshops on Molecular Visualization Date: 2 May 1997 11:35:56 -0700 Organization: U. of Mass. Lines: 112 Sender: daemon@net.bio.net Distribution: world Message-ID: <336A3432.6FB7@biochem.umass.edu> NNTP-Posting-Host: net.bio.net NOTE 1: These workshops will be attended primarily by faculty from the NORTHEASTERN USA because of the requirement to travel to Amherst MA on three (3) separate occasions at your own expense. NOTE 2: These workshops are for faculty teaching biological or biochemical subjects involving MACROmolecules, where visualization without modeling is appropriate. Chemistry faculty interested in modeling software for small molecules should consider a separate workshop, http://copper.chem.umass.edu/Lahti-stuff/NERMMW_PAGE/nermmw.html Free Workshops on Molecular Visualization for Undergraduate Bioscience Teaching Amherst MA -- Summer, 1997-8 Free, hands-on workshops will be held this summer at the University of Massachusetts in Amherst to prepare college faculty with no prior experience to use molecular visualization in their classes. Understanding the three-dimensional structures of proteins, DNA, RNA, and their interactions is difficult from flat pictures, yet grasping structure is important to understanding function. Free software is now available which displays attention-grabbing 3D animated images of biological molecules in depth-cued spacefilling color. RasMol (http://www.umass.edu/microbio/rasmol), which works on Windows or Macs, encourages self-directed exploration. Chime (http://www.umass.edu/microbio/chime) allows annotated preset views of molecules to be delivered as web tutorials. Workshop participants will travel to the Amherst campus on three separate days (two this summer, one the following summer), and are responsible for their own travel expenses (and therefore are expected primarily from the Northeastern USA). Overnight accomodations will be provided free to those needing them (based on distance traveled). Participants will be expected to incorporate molecular visualization into their teaching, and to mentor two faculty colleagues at their home institution. The workshops will be led by Eric Martz, a Professor in the Department of Microbiology. Martz has innovated molecular structure tutorials which are in use throughout the USA and in dozens of other countries. The web site he created (see above) was visited by 40,000 people in 1996. 1997 dates are June 17 and 30 (workshop A), or June 19 and July 2 (workshop B). Workshops A and B also meet for one day in late June 1998. To obtain more detailed information and a REGISTRATION FORM, visit http://www.umass.edu/microbio/rasmol/workshop.htm or FAX a request to 413-545-1578, or email a request to emartz@microbio.umass.edu. Supported by the National Science Foundation (Undergraduate Faculty Enhancement, Division of Undergraduate Education) and the University of Massachusetts. From owner-acedb@net.bio.net Sun May 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!sprout.nal.usda.gov!usenet From: Doug Bigwood Newsgroups: bionet.software.acedb Subject: CALL FOR PARTICIPATION - ACE97 CONFERENCE AND WORKSHOP Date: Mon, 05 May 1997 14:19:00 -0400 Organization: Genome Informatics Group, University of Maryland Lines: 33 Message-ID: <336E2494.2262@gig.usda.gov> NNTP-Posting-Host: locus.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) CALL FOR PARTICIPATION - ACE97 CONFERENCE AND WORKSHOP The organizers of the ACE97 Conference and Workshop invite your participation. ACE97 will take place at Cornell University in Ithaca, New York,USA from July 27, 1997 through August 9, 1997. Details concerning the conference can be found at http://probe.nalusda.gov/ace97.html. We are soliciting papers for oral presentation during the formal conference (July 28,29). Poster presentations are invited as well. Although there may be a limited amount of physical poster space at the conference it is requested that all posters be presented electronically as HTML pages on the ACE97 Web site. Papers for oral presentation can be about any ACEDB-related topic, but should concern areas such as innovative uses of ACEDB, ACEDB software enhancements, new external tools developed for use in conjunction with ACEDB, etc. Descriptions of databases which use ACEDB should be submitted as posters unless they contain unique or unusual features. Papers and posters from ACE95 can be viewed at http://probe.nalusda.gov:8000/acedocs/ace95/index.html. Submission Details: Send an abstract by electronic mail to ace97@gig.usda.gov. The Subject line should read "ACE97 Submission". Indicate whether the abstract is for a poster or an oral presentation. Papers for oral presentation will require that a full length (about two to five pages) electronic paper be submitted prior to the conference. The paper will be published on the ACE97 Web site. If your paper is not accepted for presentation then you will be encouraged to submit a poster instead. The submission deadline is June 27. Earlier submission is strongly suggested - notification of acceptance will occur immediately upon approval. Details regarding how to submit an electronic paper or poster will be sent along with your acceptance notice. From owner-acedb@net.bio.net Mon May 05 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Doug Bigwood Newsgroups: bionet.software.acedb Subject: CALL FOR PARTICIPATION - ACE97 CONFERENCE AND WORKSHOP Date: 6 May 1997 16:41:11 -0700 Organization: Genome Informatics Group, University of Maryland Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <336A01CE.7E24@gig.usda.gov> NNTP-Posting-Host: net.bio.net CALL FOR PARTICIPATION - ACE97 CONFERENCE AND WORKSHOP The organizers of the ACE97 Conference and Workshop invite your participation. ACE97 will take place at Cornell University in Ithaca, New York,USA from July 27, 1997 through August 9, 1997. Details concerning the conference can be found at http://probe.nalusda.gov/ace97.html. We are soliciting papers for oral presentation during the formal conference (July 28,29). Poster presentations are invited as well. Although there may be a limited amount of physical poster space at the conference it is requested that all posters be presented electronically as HTML pages on the ACE97 Web site. Papers for oral presentation can be about any ACEDB-related topic, but should concern areas such as innovative uses of ACEDB, ACEDB software enhancements, new external tools developed for use in conjunction with ACEDB, etc. Descriptions of databases which use ACEDB should be submitted as posters unless they contain unique or unusual features. Papers and posters from ACE95 can be viewed at http://probe.nalusda.gov:8000/acedocs/ace95/index.html. Submission Details: Send an abstract by electronic mail to ace97@gig.usda.gov. The Subject line should read "ACE97 Submission". Indicate whether the abstract is for a poster or an oral presentation. Papers for oral presentation will require that a full length (about two to five pages) electronic paper be submitted prior to the conference. The paper will be published on the ACE97 Web site. If your paper is not accepted for presentation then you will be encouraged to submit a poster instead. The submission deadline is June 27. Earlier submission is strongly suggested - notification of acceptance will occur immediately upon approval. Details regarding how to submit an electronic paper or poster will be sent along with your acceptance notice. From owner-acedb@net.bio.net Wed May 14 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: equals !!! Date: 15 May 1997 11:00:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: <9705151801.AA05081@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > > Hi Jean, there's still a problem with querying Texts. 'find image > > pick_me_to_call = display' returns no hits. Either '*display' or > > 'display*' or '"display"' works, but not without * or enclosing quotes. > > the problem comes from the fact that Display is a tag in your system Yikes! The oldest gotcha in the book. But wait... I thought this was only a problem when querying directly for objects by name. E.g. 'find colleague fax' finds colleagues with a value for tag Fax and not colleagues whose name is Fax. > your case is a bit different you say > > Pick_me = Display That's right, the "=" means I'm looking for the value of tag Pick_me to match the argument, interpreted as a literal string. But wait... > suppose you want to find fat people you say > > Size = Weight > > here you hope that weight is a tag with a numerical value > to force nunmerical evaluationyou can put [] What??!! The argument of "=" can be a tag whose _value_ is substituted? I never knew that. I can't find it in any of the xace Help or AGIS ACEDB documentation either. But it seems to be true. For these records, Trait_scores : "A" Score 9 Standard_deviation 9 Trait_scores : "B" Score 9 Standard_deviation 30 the query 'find trait_scores score = [standard_deviation]' finds A and not B. The [] are required on the right-hand-side. This doesn't work for string comparisons though. So, if there is an "=" and the argument has no [], would it be reasonable to always treat the argument as a literal string? - Dave From owner-acedb@net.bio.net Thu May 15 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re: equals !!! Date: 15 May 1997 17:03:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9705160004.AA05905@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I said: : So, if there is an "=" and the argument has no [], would it be reasonable : to always treat the argument as a literal string? Jean replies that he has now made this so. So for example 'find image pick_me_to_call = display' should work now. - Dave From owner-acedb@net.bio.net Thu May 15 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ACEDB worm data release WS2.4-20 and WG2.4-4 Date: 16 May 1997 08:15:27 +0100 Lines: 106 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5lh1if$a4b@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates WG2.4-3 to 4-4 and WS2.4-17 to 4-20 for C. elegans ===================================================================== You should be using these in conjunction with release 4_3 of the acedb software. **** WARNING **** Unfortunately, these update files increase the WS2 database size on disk to around 700Mb. We have been trying to find a way to reduce this, which has led to the delay in this release. We plan to make another release before the Madison Worm Meeting (May 28 - June 1), and hope that will use less disk space. ***************** Reminder: there are now two versions of the C.elegans database. The WS2 update series contains everything, whereas WG2 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG2.4-2 and WS2.4-16 are: for both types of update - a fix to the map displays which were behaving oddly - the expression pictures with the display script from wscripts/ that was missing in the initial WS/G2 release. (the next update will have bibliography, genetics, embl etc (as usual) and for just the complete database including sequences (WS2.4-17 plus) Data fom St Louis and Sanger Sequence databases taken in mid-Apr: - There are now 2177 ( 2020 before) cosmids totalling 65222006 (60615799 before) bases. - Peptides have been updated only to include new ones. The total database sizes after adding these updates are around 700Mb for the WS2 database and around 65Mb for the WG2 database. It will take time to read in the WS2 updates, perhaps 2-3 hours. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_3.tar.Z # get program cd ../celegans # change to worm data directory mget update.WS1.* # get all WS1 update files quit -------------------------------- Get any update files that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Thu May 15 23:00:00 1997 Path: biosci!daresbury!uninett.no!news.uni-c.dk!news.uni-c.dk!not-for-mail From: Jan Hansen Newsgroups: bionet.software.acedb Subject: Prediction of O-glycosylation sites Date: Fri, 16 May 1997 14:17:48 +0200 Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 51 Message-ID: <337C506C.59E2@cbs.dtu.dk> NNTP-Posting-Host: dna.cbs.dtu.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.2 IP22) Prediction of Mucin type O-glycosylation sites, NetOglyc version 2.0: NetOglyc is a neural network algorithm recognizing Mucin type O-glycosylation sites in mammalian proteins. The method have been updated with increased performance. The method is available at: http://www.cbs.dtu.dk/services/NetOGlyc/ both as a mail and www server. The in vivo glycosylations sites used for making the method is listed in O-GLYCBASE available at: http://www.cbs.dtu.dk/databases/OGLYCBASE/ Abstract: The specificities of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase family which links the carbohydrate GalNAc to the side chain of certain serine and threonine residues in mucin type glycoproteins are presently unknown. The specificity seems to be modulated by sequence context, secondary structure and surface accessibility. The sequence context of glycosylated threonines was found to differ from that of serine, and the sites were found to cluster. Non-clustered sites had a sequence context different from that of clustered sites. Charged residues were disfavoured at position -1 and +3. A jury of artificial neural networks was trained to recognize the sequence context and surface accessibility of 299 known and verified mucin type O-glycosylation sites extracted from O-GLYCBASE. The cross-validated NetOglyc network system correctly found 83 % of the glycosylated and 90 % of the non-glycosylated serine and threonine residues in independent test sets, thus proving more accurate than matrix statistics and vector projection methods. -- Jan Hansen Center for Biological Sequence Analysis Department of Physical Chemistry The Technical University of Denmark Building 206 DK-2800 Lyngby Denmark Phone: +45 4525 2485 Fax: +45 4593 4808 E-mail: janhan@cbs.dtu.dk WWW: http://www.cbs.dtu.dk/janhan/homepage.html From owner-acedb@net.bio.net Thu May 15 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: ACE97 Registration is now open Date: 16 May 1997 14:38:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 242 Sender: daemon@net.bio.net Distribution: world Message-ID: <9705162139.AA07381@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net The Registration form for ACE97 has now been placed on the ACE97 Home Page, http://probe.nalusda.gov:8000/ace97.html. A text copy is appended below. Please note that you cannot register by email. Payment must accompany the registration form, either a check or a signed credit card authorization as hard copy (or fax). If in addition you feel an urge to send a copy of the registration by email you may do so (matthews@greengenes.cit.cornell.edu), and it would be somewhat helpful in our planning. But the required form is the paper one. We're looking forward to welcoming you to Ithaca and ACE97 !! - Dave ============================================================================ ACE97 Conference and Workshop Ithaca, NY, July 27 - August 9, 1997 Registration and Housing ============================================================================ Please print out this form and mail or fax it with payment by July 7, 1997 to: Cornell Conference Services / ACE97 206 Robert Purcell Community Center Ithaca, NY 14853-6001, USA Fax: 607-255-4722 Credit card authorizations via fax can be accepted, but not via e-mail or voice phone. For up-to-date information on ACE97 please consult the ACE97 Home Page, http://probe.nalusda.gov:8000/ace97.html ============================================================================ Name __________________________________________________________________ Address __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Phone _______________________ _______________________ ________________ Work Home Fax Email ____________________________ Social Security number _______________ Guests'__________________________________________________________________ names Emergency contact (not _________________________________ _______________________________ attending Name Phone numbers ACE97) Special __________________________________________________________________ needs Description of your ACEDB-related activities, for the ACE97 Home Page and Proceedings: _________________________________________________________________________ _________________________________________________________________________ _________________________________________________________________________ _________________________________________________________________________ ============================================================================ TUTORIALS There will be four tutorial sessions on the first day of ACE97, 2 morning and 2 afternoon. To help us schedule the topics to minimize conflicts, please indicate which of the tentative topics below you wish to attend. _____ New Curators - How to Create an ACeDB Database - Sam Cartinhour Advanced Curators - Making use of ACeDB displays - (Unknown) _____ Part 1: Map displays _____ Part 2: Sequence display _____ An Introduction to Java and Applets - John Morris _____ ACEDB for Windows - Richard Bruskiewich Setting up a WWW interface to ACEDB _____ Part 1: Setting up an aceserver - Curt Jamison _____ Part 2: Webace - Steve Beckstrom-Sternberg _____ Acembly, Sequence Assembly Program - Jean Thierry-Mieg _____ GeneFinder and ACeDB - Richard Durbin Querying _____ ACEDB query language _____ Tablemaker _____ Other suggestions ___________________________________________ ============================================================================ ARRANGEMENTS Registration There are three options for Registration, depending on which portions of the Program you wish to attend. * 3-Day: Tutorials and Conference only * 6-Day: Including the first few days of the Workshop as well * 14-Day: The entire meeting All registrations include the Monday night Barbecue. The 14-Day plan includes the Banquet Thursday, Aug. 5. Guests are spared the cost of the daily coffee breaks. Participants: 3-Day _______ people x $ 50.00 = $ _____________ 6-Day _______ people x $ 80.00 = $ _____________ 14-Day _______ people x $180.00 = $ _____________ Guests: 3-Day _______ people x $ 40.00 = $ _____________ 6-Day _______ people x $ 60.00 = $ _____________ 14-Day _______ people x $150.00 = $ _____________ All 14-Day Registrants: For the Banquet there is a choice of entree: * Braised Chicken with Lemon and fresh Thyme, served on a bed of caramelized sweet onions * Grilled Veal Chop with a Portabella fresh Thyme jus lie Please indicate your choices below. (We must have this information by the registration deadline.) Veal ______________________________________________________ Chicken ______________________________________________________ Names Housing Inexpensive housing has been arranged in Cascadilla Hall, a residence hall close to the meeting rooms. See below for details and other options. Arrival date ________________ Departure date _____________________ Single occupancy ____ people x $23.50/night x_____ nights = $__________ Double occupancy ____ people x $20.50/night x_____ nights = $__________ Total housing = $__________ For double occupancy: Roommate name ______________________________ Meals The room rate in Cascadilla Hall includes continental breakfast each day. Other meals are on your own. The "Collegetown" area of inexpensive, moderate, and/or fast dining establishments is nearby, and more sumptuous opportunities are available downtown (six blocks, and one of Ithaca's famous hills). Parking Parking is available one block west (downhill) from Cascadilla Hall for approximately $4.00/day. Please let us know if you plan to have a car so we can obtain a parking sticker for you. Yes _____ No _____ ============================================================================ PAYMENT Full payment must accompany this form. If paying by credit card, please provide account number and authorized signature. Cornell will accept only the three cards indicated below. Checks or money orders should be made payable to Cornell University, and be payable in US dollars. Foreign participants must use a credit card, or submit a bank check (not a personal check). For credit card payment, a PAPER copy of your signature is required. Fax is acceptable but not email or voice phone authorization. ___Visa ___MasterCard ___American Express ____________________________________ Credit card number Name as shown on card_________________________________ Expiration date ________ Signature ____________________________________________________ There is a $25.00 fee for cancellations prior to July 11, and a $25.00 fee will be charged for any returned check or invalid credit card charge. NO REFUNDS CAN BE GIVEN FOR CANCELLATIONS AFTER JULY 11, 1997. ============================================================================ ACE97 HOUSING DETAILS Cascadilla Hall Cascadilla Hall is one of the oldest student residences at Cornell, and one of the most recently renovated, retaining its classic exterior but making it very comfortable and attractive inside. Perched on the edge of scenic Cascadilla Glen, it is conveniently located less than a block from the Hollister Computer Facility to the north and the Collegetown eating / shopping / services area on the south. One floor of Cascadilla Hall (45 rooms) has been reserved for us. The rooms are equipped with telephones, and local calls are free. Housekeeping service consists of bed linens and a towel exchange once per week. It does not include daily bed making, room cleaning, or wake-up call service. The Hall is not air conditioned. If the weather is warm, electric fans are available for rent ($12). To reserve a room in Cascadilla Hall, fill out the Housing section of the form above and submit it with your registration. Other housing options Other housing within a block or two of the ACE97 activities includes * Collegetown Motor Lodge, 607-273-3542, Fax 607-272-3542 In Collegetown. Reasonable. * Statler Hotel, 607-257-2500 or 800-541-2501 Operated by the Cornell School of Hotel Administration. Nicer, more expensive. For those with cars, many other options are within a short drive. A good summary of lodging in the Ithaca area is on the IthacaNet Web page, http://www.ithaca.ny.us/. To make reservations at one of these other locations, please contact it directly. ============================================================================ From owner-acedb@net.bio.net Sun May 18 23:00:00 1997 From: (DogZ Software Center) Newsgroups: bionet.software.acedb Subject: Microsoft Office 97 costs US$45 ? 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If you want some more details , you can go http://www.hkstar.com/~dogz now. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DogZ Software Center From owner-acedb@net.bio.net Sun May 18 23:00:00 1997 From: (DogZ Software Center) Newsgroups: bionet.software.acedb Subject: MS Office 97 only costs US$45?! Shopping Paradise Date: Tue, 20 May 1997 04:52:33 GMT Organization: Netvigator Lines: 60 Message-ID: <5lpiet$vb8@imsp009a.netvigator.com> NNTP-Posting-Host: hhtam010039.netvigator.com X-Newsreader: Forte Agent .99b.112 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!europa.clark.net!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!news2.hkt.net!news.hkt.net.!imsp009a.netvigator.com!locker Windows 95, Visual Foxpro, MS Office 7.0, Visual Basic, Visual C++, Borland C++, Lotus cc:Mail Release 6, Lotus SmartSuite 97, ...... only costs US$45 for all? MS Office 97 only costs US$45! Hong Kong is the paradise in shopping. You can buy anything you want by an reasonable price. Today, by this chance, we would like to introduce to those who are interest in computing. In Hong Kong, there are five famous spots inclues: Golden Center - Sham Shui Po ; Mongkok Computer Center - Mongkok ; Sino Center - Mongkok ; 298 Computer Center - Wan Chai and Tsuen Fung Center -Tsuen Wan . In which, you can always find the most update warez includes all PC Warez, PC games, CD-Title, Shareware, Video-CD and Playstation game, etc. For Example, Inside a Installer (one CD only, Product No.: IN96112) , it contains MS Visual Foxpro 5.0, MS Windows 95 OEM Service Release, MS Money97, Lotus SmartSuite 97, Lotus cc:Mail Release 6, Symantec Cafe 1.5, Norton Your Eyes Only, Norton Smart Doctor 1.0, Quartdeck SpeedyROM 1.1, KPT BrayceAlpha 2.0, Visual dBASE Professional 4.4a, MacroMedia Animator Designer, Solitaire Antics, Almost Reality, CakeWalk Express 3.01, ClockMan95, Demo-It!2.0, MicroLogic EMAGIC, EXTRA! Version 6.2, MacroMedia Icon Designer, Infinite Disk, InfoSpy Pro, Fractal Deign Ray Dream Studio 4.1, Janna Conract Manager, Kurzweil Voice release 2.0, PC Maclan verion 6.0, NetWizard Plus Version 3.1, Organic Art, Microsoft Edition, PhotoWorks, RandoMedia, Real Oschestra, Reflection 4, RichWin, SoundForge 4.0, SignLab Pro+, Spectrum Pro CD Player, Starfish Internet Sidekick, TeleMagic, TurboCAD 3.0, MS-Visual SourceSafe 5.0, WinBye 32, Xing 3.02 Release, Zydeco Management Desktop. Good news to you today, that is, we would like to introduce all wares in VERY attractive price to you. Not only to provide over 50 warez for you to choose, but also to introduce the most suitable warez to you. We would provide a very attractive price not more than US$50. The more you buy, the more money you can save. Right? Hurry up! Don't miss this chance! Just ask what you want to know OR just decide and place your order to us. If you want some more details , you can go http://www.hkstar.com/~dogz now. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DogZ Software Center From owner-acedb@net.bio.net Sun May 18 23:00:00 1997 From: (DogZ Software Center) Newsgroups: bionet.software.acedb Subject: MS Office 97 only costs US$45?! Shopping Paradise Date: Tue, 20 May 1997 04:58:54 GMT Organization: Netvigator Lines: 60 Message-ID: <5lpiqq$sn8@imsp009a.netvigator.com> NNTP-Posting-Host: hhtam010039.netvigator.com X-Newsreader: Forte Agent .99b.112 Path: biosci!daresbury!uninett.no!nntp.uio.no!Norway.EU.net!EU.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!news2.hkt.net!news.hkt.net.!imsp009a.netvigator.com!locker Windows 95, Visual Foxpro, MS Office 7.0, Visual Basic, Visual C++, Borland C++, Lotus cc:Mail Release 6, Lotus SmartSuite 97, ...... only costs US$45 for all? MS Office 97 only costs US$45! Hong Kong is the paradise in shopping. You can buy anything you want by an reasonable price. Today, by this chance, we would like to introduce to those who are interest in computing. In Hong Kong, there are five famous spots inclues: Golden Center - Sham Shui Po ; Mongkok Computer Center - Mongkok ; Sino Center - Mongkok ; 298 Computer Center - Wan Chai and Tsuen Fung Center -Tsuen Wan . In which, you can always find the most update warez includes all PC Warez, PC games, CD-Title, Shareware, Video-CD and Playstation game, etc. For Example, Inside a Installer (one CD only, Product No.: IN96112) , it contains MS Visual Foxpro 5.0, MS Windows 95 OEM Service Release, MS Money97, Lotus SmartSuite 97, Lotus cc:Mail Release 6, Symantec Cafe 1.5, Norton Your Eyes Only, Norton Smart Doctor 1.0, Quartdeck SpeedyROM 1.1, KPT BrayceAlpha 2.0, Visual dBASE Professional 4.4a, MacroMedia Animator Designer, Solitaire Antics, Almost Reality, CakeWalk Express 3.01, ClockMan95, Demo-It!2.0, MicroLogic EMAGIC, EXTRA! Version 6.2, MacroMedia Icon Designer, Infinite Disk, InfoSpy Pro, Fractal Deign Ray Dream Studio 4.1, Janna Conract Manager, Kurzweil Voice release 2.0, PC Maclan verion 6.0, NetWizard Plus Version 3.1, Organic Art, Microsoft Edition, PhotoWorks, RandoMedia, Real Oschestra, Reflection 4, RichWin, SoundForge 4.0, SignLab Pro+, Spectrum Pro CD Player, Starfish Internet Sidekick, TeleMagic, TurboCAD 3.0, MS-Visual SourceSafe 5.0, WinBye 32, Xing 3.02 Release, Zydeco Management Desktop. Good news to you today, that is, we would like to introduce all wares in VERY attractive price to you. Not only to provide over 50 warez for you to choose, but also to introduce the most suitable warez to you. We would provide a very attractive price not more than US$50. The more you buy, the more money you can save. Right? Hurry up! Don't miss this chance! Just ask what you want to know OR just decide and place your order to us. If you want some more details , you can go http://www.hkstar.com/~dogz now. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DogZ Software Center From owner-acedb@net.bio.net Mon May 19 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: daj@nhm.ac.uk (david johnston) Newsgroups: bionet.software.acedb Subject: A problem in MacAce? Date: 20 May 1997 12:21:38 +0100 Lines: 41 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ls1g2$qqm@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Greetings all. We have just released the first version of an acedb database to support the schistosome genome project and one of our users reports the following problem trying to run it using MacAce. He managed to set up the database, read in the data etc. successfully .We have a class "Readme" which provides simply for longtext descriptions of various things (like lists of the contents of the release), literally its model is: ?Readme Document ?LongText When our user tried to open one of these, his machine "freezed, started ringing, blinking and displayed a message "Invalid action ###### received in drawBox()". I would appriciate if anyone could provide suggestions as to what the problem is/ how to solve it. He is using PowerBook as a hardware with PowerPC 603e 167Mz and 32Mb RAM. I run the database on a Powerbook 5300 and haven't experienced this problem. Thank you in advance. David. David A. Johnston, Secretary to the WHO Schistosoma Genome Network, Biomedical Parasitology Division, Dept. of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, England, UK. Tel: 0171 9389297 (from outside the UK: 44 171 9389297) Fax: 0171 9388754 (from outside the UK: 44 171 9388754) eMail daj@nhm.ac.uk The Biomedical Parasitology Division is a WHO Collaborating Centre for the identification of schistosomes and their snail hosts. From owner-acedb@net.bio.net Mon May 19 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: mieg@vega.crbm.cnrs-mop.fr (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: ?Readme Date: 20 May 1997 12:47:21 +0100 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ls309$sk8@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk two questions: 1) does the machine freeze when one open the Readme object or the corresponding longtext 2) is it specific to the mac , or also visible on other platforms 3) what code exactly is beeing run From owner-acedb@net.bio.net Tue May 20 23:00:00 1997 Path: biosci!wpo.pi.sa.gov.au!dale.debbie From: dale.debbie@wpo.pi.sa.gov.au Newsgroups: bionet.software.acedb Subject: Images in WinAce Date: 20 May 1997 23:26:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net ** High Priority ** Hi all. I am in the process of setting up a new database using the Win95 version of ACeDB, and wondered if anyone out there knows how to get it to display images? Does it still use the old "pick_me_to_call"....? Thanks for your help. Debbie From owner-acedb@net.bio.net Tue May 20 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!news.starnet.net!news.starnet.net!newsreader.wustl.edu!not-for-mail From: T Harter Newsgroups: bionet.software.acedb Subject: database update for Winace Date: Wed, 21 May 1997 10:36:42 -0500 Organization: Washington University in St. Louis Lines: 6 Message-ID: <3383168A.7A6EB7F3@umslvma.umsl.edu> NNTP-Posting-Host: op0157.wustl.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b4 [en] (Win95; I) X-Priority: 3 (Normal) How do I update the database using Windows for my OS? ------------------------ Theresa Harter - Washington University Medical School harter@am.seer.wustl.edu ------------------------ From owner-acedb@net.bio.net Tue May 20 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Matt Couchman Newsgroups: bionet.software.acedb Subject: Dumping tables from tace Date: Wed, 21 May 1997 16:32:16 +0100 Organization: The John Innes Centre Lines: 9 Message-ID: <33831580.41C6@bbsrc.ac.uk> NNTP-Posting-Host: jiio5.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V3.2 alpha) Hello, I'm looking for a tace equivalent to the xace tablemaker's "ascii dump" command (Where the table is dumped to a text file delimited by the character of the user's choice). Can anyone help? Thanks very much, Matt. From owner-acedb@net.bio.net Wed May 21 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.software.acedb Subject: IMPORTANT - BIOSCI moving to Stanford! Date: 21 May 1997 20:42:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 55 Sender: daemon@net.bio.net Distribution: world Message-ID: <199705220342.UAA01880@net.bio.net> NNTP-Posting-Host: net.bio.net After more than a decade of serving the biology community on the BIOSCI project, I have decided that it is time for me to pass the torch. The demands of my career and family are making it increasingly difficult for me to run BIOSCI adequately on a part-time basis, and I've decided that I would do the project more harm than good by clinging to it. Therefore I have concluded an agreement with the Stanford University Libraries to take over the management of the BIOSCI project effective 6 June 1997. Many of you know the work of the Stanford Libraries through HighWire Press which has done an excellent job bringing the Journal of Biological Chemistry, Science Magazine, and other prestigious journals to the WWW (see http://highwire.stanford.edu/). I have every confidence that Stanford will provide an environment where the BIOSCI project can flourish. The BIOSCI team at Daresbury will continue to support the project in Europe, and Dave Mack and Julie Lawrence on the current BIOSCI staff will continue to assist the new team at Stanford. The project will be managed by Serge Taylor of the Stanford Libraries who is responsible for developing Web-based "knowledge environments" for scientists. I will still participate with the project in an advisory capacity but have to phase myself out of day-to-day operations. Many of you who read bionet.announce, bionet.biology.computational, and bionet.jobs.offered (the groups that I moderate) have been aware of the recent posting delays that my busy schedule has inflicted on those newsgroups. I am pleased to announce that Todd McGee, Scientific Advisor of the HighWire Press, will be taking over moderation of those groups from me this week. ** NOTE ** - The BIOSCI hardware will be down for backups on 6 June and will be moved over the weekend of June 7 and 8. We will be changing the IP number of the machine, but the host name and all mailing addresses will remain unchanged. There may be a few days of service disruption during this time due to the move unfortunately, just as we experienced in BIOSCI's previous move. We hope to keep this to a minimum. We will post status reports on the move to bionet.announce before and after it happens. Please watch that newsgroup for details. It has been a pleasure serving all of you since the "early days" of biology on the Internet. I've had the pleasure of not only "knowing" many of you over the Internet, but have also met literally thousands of biologists around the U.S. and elsewhere during the many Internet training seminars that I gave over the last decade. I've been truly fortunate to have been given the chance to play a role in the growth of biology on the Internet. This is something I will always treasure. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-acedb@net.bio.net Mon May 26 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ACEDB worm data release WS3.4-17 Date: 27 May 1997 03:20:59 +0100 Lines: 145 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5mdgeb$jkg@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk ** WARNING: This release is only complete at the NCBI site in the USA. ** We plan to bring the UK and France sites up to date within the next ** day or two. This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. New ACEDB data release WG3.4-2 and WS3.4-17 for C. elegans ========================================================== With this release we are once again starting a new series of database updates from scratch again, rather than adding on to WS2.4-20. The new series is called WS3 (and correspondingly WG3 for the version without sequences). Because both series are new, you must get all the updates from the series you want (WS3 or WG3), and rebuild a new database using them. Fortunately, it will be much faster reading in the seventeen new WS3 updates than twenty-four of the WS2 series. (N.B. at the end of this file is a list of the contents of each update file). If you have a working acedb version built with the WS2 series, you must do two things: (1) you must remove your current database/ directory (ideally after backing it up in case of difficulties). As well as removing the database directory, you can also remove any update.WS2...tar.Z or rawdata/update.WS2... files. (2) you must get a new copy of the INSTALL script, as well as all the new WS3 updates. If you do not remove the contents of the database directory, when you start up acedb it will still say "WS2" in the title bar, and will not be able to load the WS3 updates. When you have emptied it properly, it will ask if you want to reinitialise, and put WS3 in title bar. The software has not changed. You should be using these updates in conjunction with release 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS3 update series contains everything, whereas the WG3 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since the last release are: for both types of update - a physical map update with a few changes (mid May) - accumulated genetic data corrections - from CGC : bibliography, wbg subscribers and strains (May) - from Leon Avery : worm meeting absracts with connections to genes etc. and for just the complete database including sequences (WS3.4-17) Data fom St Louis and Sanger Sequence databases taken in mid-May: - There are now 2237 (2177 before) cosmids totalling 66969575 (65222006 before) bases. - EMBL50 Sequence, dna and full embl text descriptions The total database sizes after adding these updates are around 560MB for the WS3 database and around 60MB for the WG3 database. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_3.tar.Z # get program cd ../celegans # change to worm data directory mget update.WS3.* # get all WS1 update files quit -------------------------------- Get any update files that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) UPDATE FILE CONTENTS (BRIEFLY) ws3.4-1 = geneace 1st half (i.e. non sequence material) ws3.4-2 = geneace 2nd half (i.e. non sequence material) ws3.4-3 = file1 (sequence_ace bits & pieces) ws3.4-4 = peptide file ws3.4-5 = dna1 ws3.4-6 = dna2 ws3.4-7 = dna3 ws3.4-8 = dna4 ws3.4-9 = dna5 ws3.4-10 = protein1 ws3.4-11 = protein2 ws3.4-12 = protein3 ws3.4-13 = sequence1 ws3.4-14 = sequence2 ws3.4-15 = sequence3 ws3.4-16 = sequence4 ws3.4-17 = sequence5 & motif & general fixes From owner-acedb@net.bio.net Mon May 26 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!feeder.chicago.cic.net!newsxfer.nether.net!newsxfer3.itd.umich.edu!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!marlin.ucsf.edu!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Curator) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 27 May 1997 22:31:22 GMT Organization: Dept. Plant Breeding, Cornell University Lines: 1362 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <5mfnbq$j8b@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.psw.fs.fed.us Summary: Frequently Asked Questions about finding and getting started with the genome database software ACEDB. URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 27 May 97 Version: 1.37 ---------------------------------------------------------------------------- ACEDB FAQ ---------------------------------------------------------------------------- Curated by: Dave Matthews ---------------------------------------------------------------------------- Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : What is the current version of ACEDB? * Q2 : What hardware/software do I need to run ACEDB? * Q3a : Where can I get ACEDB? * Q3b : + Where can I get the graphic ace client? * Q4 : How does ACEDB compare to commercial relational DBMS's? * Q5 : Is ACEDB object-oriented? * Q6 : What documentation exists for ACEDB? * Q7 : What other resources are available for ACEDB? * Q8 : How should ACEDB be cited? * Q9 : How does one get on/off the ACEDB announcements mailing list? * Q10 : ! When and where is the next ACEDB Workshop? * Q11 : ! What ACEDB databases exist? * Q12 : Who prepared this document & where is the current version? Questions marked with '+' are new, those with '!' have substantially changed answers. ---------------------------------------------------------------------------- Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q11 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: (This answer refers to the software, not the C. elegans data.) Current Unix version is 4_3 (as of May 1996) and is identical to the test version test.4_3i. A Macintosh version is available as version 4.1b1. A Windows 95/NT version is available as version beta960927. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions ---------------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. * Unix: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux o NEC EWS4800 o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/NT * Macintosh (not currently supported) Return to List of Questions ---------------------------------------------------------------------------- Q3a: Where can I get ACEDB? A3a: Source code and Unix binaries are available in the following anonymous ftp sites: * lirmm.lirmm.fr in pub/acedb * ftp.sanger.ac.uk in pub/acedb * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Linux binaries in ELF and a.out format, from Jeff Bryer: * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb NEC EWS4800 binaries: * http://www.labs.nec.co.jp/freesoft/freesofte.html Windows 95/NT 3.51, from Richard Bruskiewich: (Note: This is a development version, not fully debugged.) * ftp.sanger.ac.uk in pub/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: (Note: The authors are not currently able to support MacAce. Latest version was 4.1b1.) * genome.lbl.gov in pub/macace * ncbi.nlm.nih.gov in repository/acedb/macace * bioinformatics.weizmann.ac.il in pub/databases/acedb Return to List of Questions ---------------------------------------------------------------------------- NEW! Q3b: Where can I get the graphic ace client? A3b: from Jean 15apr97: I have now a graphic client with read write access and i would be happy to have people test it, it runs off any unix platform, including linux and is good if several people want to update in parallel or to have distant users To obtain the client, send mail to Jean, mieg@kaa.crbm.cnrs-mop.fr. ---------------------------------------------------------------------------- Q4: How does ACEDB compare to commercial relational DBMS's? A4: From Jean Thierry-Mieg, 4/97: Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developed at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzzy answers, that one tries to refine progressively. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommend sybase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of de-correlated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availability of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows (in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sybase. 5) Ease of use, i seriously believe that ace is much easier to configure and use than sybase. _____________________ Finally one should consider the following question: concurrency. Sybase has a well designed transaction system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifications are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independent data in parallel. This is now well tested. A graphic client system is being developed and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joins. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests run on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sybase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Return to List of Questions ---------------------------------------------------------------------------- Q5: Is ACEDB object-oriented? A5: From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------------- Q6: What documentation exists for ACEDB? A6: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: * acedb -- A C. elegans Database: I. Users' Guide. * acedb -- A C. elegans Database: II. Installation Guide. * acedb -- A C. elegans Database: III. Configuration Guide. * Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z. The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp http://www.cbi.or.jp/~sano/ . (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.nih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). URL : http://genome-www.stanford.edu/docs/aatdb_man.html. A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. URL : http://probe.nalusda.gov:8000/acedocs/overview.html. Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. Return to List of Questions ---------------------------------------------------------------------------- Q7: What other resources are available for ACEDB? A7: Perl and WWW tools The AGIS server at the National Agricultural Library provides tools for integrating version ACEDB with perl and the World-Wide Web. A WWW interface to 4.3 is available as ftp://probe.nal.usda.gov/pub/tools/webace.tar.gz. Instructions for this interface can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html. (An earlier tool set is available as ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz). For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. Java Interface A Java interface to acedb is under active development. Involved people are Lincoln Stein, Jean Thierry-Mieg, Doug Bigwood, John Barnett, Sam Cartinhour. A test system can be seen at http://alpha.crbm.cnrs-mop.fr If you are interested in this approach, please contact mieg@kaa.crbm.cnrs-mop.fr X-client The 4_3 distribution contains the source code for a new version of the code called xclient. You need to recompile it (make xclient). Then, you create an empty database with the nematode models and strat xclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the montpellier server in the distrib server.wrm). The data will be saved locally and can then be viewed with a normal xace. The control of which data should be imported is very crude. In anay session, every object will be imported once. This should be rationalised, please let us know if this approach seems useful, and how it should be configured. (mieg@kaa.crbm.cnrs-mop.fr) The Developers' Archive Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases via gopher at ftp://genome-ftp.stanford.edu/pub/acedb_dev/ If you have a contribution send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles in biosci.software.acedb are archived by Biosci at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb. And more Several ACEDB databases are available on the WWW via the Agricultural Genome Information System (AGIS) at the US National Agricultural Library, URL http://probe.nalusda.gov:8000/index.html. You will also find a selection of models.wrm files (schemata) for the various databases here. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: * http://moulon.inra.fr/acedb/acedb.html for C. elegans data * http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data * http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: * flydb - LBL's Drosophila Acedb-style database * 21bdb - LBL's Human Chromosome 21 Acedb-style database * querdb - LBL's query-language extensions to Acedb * metadata - LBL's compendium of Acedb database schema variants * macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version * There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to databases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: * 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). * 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier (Jean Thierry-Mieg et al), and the Integrated Genome Database project in Heidelberg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------------- Q8: How should ACEDB be cited? A8: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------------- Q9: How can I get on/off the ACEDB announcements mailing list? A9: To get on or off the mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q7 for details] is on the mailing list. Return to List of Questions ---------------------------------------------------------------------------- Q10: When and where is the next ACEDB Workshop? A10: The ACE97 Conference and Workshop will be held July 27 - August 9 in Ithaca, New York, USA. NEW! Registration for ACE97 is now open. See the ACE97 Home Page for details. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html. A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions ---------------------------------------------------------------------------- Q11: What ACEDB databases exist? A11: In alphabetic order by Database name [Curators, please submit changes as new paragraphs. You may include html links.] Database : AaeDB Species : Aedes aegypti (yellow fever mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AalDB Species : Aedes albopictus (Asian tiger (forest day) mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AtDB Species : Arabidopsis thaliana ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4-7 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/AtDB FTP : ncbi.nlm.nih.gov in repository/AtDB WWW : http://genome-www.stanford.edu FAQ_updated : December 1996 Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 WWW : http://www.biochem.kth.se/AboutDB.html FAQ_updated : July 1995 Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@sanger.ac.uk Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : August 1995 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z FAQ_updated : March 1994 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : July 1995 Database : AgaDB Species : Anopheles gambiae (malaria mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AtrDB Species : Aedes triseriatus (Eastern tree hole mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : BrassicaDB Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid species ACEDB_version : 4.3 Description : Genetic maps of Brassica napus, QTL analyses for agronomic traits, literature references and B. napus-specific DNA sequences will be incorporated. We aim to integrate with B. napus genetic maps developed elsewhere and to produce a Java interface that will link BrassicaDB with the AAtDB (Arabidopsis thaliana) database through gene orthologies that are becoming established between these closely related plant genomes. PI : Martin Trick, Martin.Trick@bbsrc.ac.uk Curator/Developer : Mazda Hewitt, Mazda.Hewitt@bbsrc.ac.uk WWW : http://nasc.nottm.ac.uk Data_updated : Under development Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : August 1995 Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edu ACEDB_version : 3.0 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : January 1996 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 ACEDB_version : 3.0 Data_version : January 1995 (version 95.1) FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ FAQ_updated : January 1995 Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated : In development FAQ_updated : November 1996 Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : CupDB Species : Culex pipiens ACEDB_version : 4.3 WWW : currently unavailable via www Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : Cyanoace Species : Cyanobacterium synechocystis sp. strain PCC6803 Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp Comment : Converted to ACEDB from Sybase FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface uses Java enhanced clickable maps. FAQ_updated : December 1996 Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database: FilDB Species: Filarial nematodes PI: Mark Blaxter ACEDB_version: 4.3 Curator: Martin Aslett Contact: Mark Blaxter, mark.blaxter@ed.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : May 1995 Database : GrainGenes Species : Wheat, barley, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu Curator : Gerard R. Lazo, lazo@pw.usda.gov PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_3 (Unix), 4.1b1 (MacAce) Data_version : 1.7, December 1996 Availability : UNIX and Macintosh versions via anonymous ftp Availability : Macintosh version on CD-ROM "RiceMac / MacGrainGenes", from Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University, Yongin, Korea. FTP : probe.nalusda.gov in pub/graingenes FTP : grain.jouy.inra.fr in pub/database Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Data_updated : December 1996 FAQ_updated : December 1996 Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database: Leishdb Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others PI: Jennie Blackwell PI: Al Ivens ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development) Data_updated: October 1996 FAQ_updated : November 1996 Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Content : Maps, raw map data, loci, probes, genetic stocks, variations, mutant images, agronomic traits, gene products, QTL, bibliography, colleague addresses; hardlinks to sequence and germplasm databases. Latest_release : Oct 1996 Acedb_version : 4.1 Curator : Mary Polacco, maryp@teosinte.agron.missouri PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz WWW : http://www.agron.missouri.edu WEBACE : http://probe.nalusda.gov:8300/ Contact : db_request@teosinte.agron.missouri.edu Comment : Data are periodically extracted into ACEDB format from Sybase Comment : Genera software used to maintain the Sybase database and its gateways, except for ACEDB Comment : ACEDB releases are announced on the MAIZE bulletin board; http://www.bio.net/hypermail/MAIZE/ Comment : WEBACE records are hardlinked to the Sybase server where data are curated Funding : USDA ARS Plant Genome Research Program FAQ_updated : Mar 7, 1997 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : July 1995 Database : Millet Genes Species : Pennisetum glaucum (Pearl Millet) ACEDB_version : 4.3 Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet WWW : http://nasc.nott.ac.uk:8400/db.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : March 1997 DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD FAQ_updated : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr ACEDB_version : 4.3 Data_version : 4-22 (December 1996) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : December 1996 Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html FAQ_updated : September 1995 Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 FTP : ftp.sanger.ac.uk in pub/PomBase FAQ_updated : September 1995 Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : November 1996 Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4.6 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Curator : Yankai Jia, jia@genome.stanford.edu Programmer : Gail Juvik, gjuvik@genome.stanford.edu Programmer : Shuai Weng, shuai@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu FAQ_updated : September 1996 Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 4.3 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_updated : April 1996 FAQ_updated : April 1996 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker, rcsshoe@iastate.edu Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://macgrant.agron.iastate.edu FAQ_updated : October 1995 Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FAQ_updated : October 1994 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html Data_updated: October 1996 FAQ_updated: November 1996 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ FAQ_updated : May 1996 Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville ACEDB_version: 4.3 Curator: Howard Cobb Curator: Martin Aslett Contact: Sara Melville, sm160@mole.bio.cam.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: October 1996 FAQ_updated: November 1996 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html FAQ_updated : April 1994 Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ FAQ_updated : August 1995 Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions ---------------------------------------------------------------------------- Q12:Who prepared this document & where is the current version? A12: This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The WWW version of this document is at: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html A text version is available via anonymous ftp at machine rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman. Major contributions in getting it off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour It is currently maintained by Dave Matthews. Please cite as: Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1996, approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions ---------------------------------------------------------------------------- From owner-acedb@net.bio.net Fri May 30 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.gsl.net!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: krishnas@aol.com (Krishnas) Newsgroups: bionet.software.acedb Subject: FREE Report on YEAR 2000 Date: 31 May 1997 03:57:41 GMT Lines: 18 Message-ID: <19970531035700.XAA18794@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear friends, We are preparing a comprehensive report on Year 2000 and in regards to that we are collecting information worldwide from everyone involved in these projects. If you are a Y2K solution provider or Working on Year 2000 projects or Contain a list of Y2K links or Interested in working on Y2K projects or Developed Y2K tools or Carrying any related information or Willing to share your experiences in handling the Y2K related problems for different industry sectors, please send us an e-mail to krishnas@aol.com We shall guarantee a copy of the complete report to everyone who provides us the feedback. Please share your valuable information and help us educate others on this issue. Krishna From owner-acedb@net.bio.net Sat May 31 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Jun 1997 02:00:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706010900.CAA17187@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net